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\subsubsection{Burst search in FRETBursts}
\label{sec:burstsearch_code}
After Following background estimation,
the burst search is the next
fundamental step of
the analysis.
In FRETBursts,
the a standard burst search on a single photon stream
(section~\ref{sec:burstsearch_intro}) (see section~\ref{sec:burstsearch_intro}) is performed
by calling the
\href{http://fretbursts.readthedocs.org/en/latest/data\_class.html#fretbursts.burstlib.Data.burst\_search}{\texttt{burst\_search} method}.
For
example example, the following command:
\begin{verbatim}
d.burst_search(F=6, m=10, ph_sel=Ph_sel('all'))
...
local rate (\verb|m=10|).
A different photon selection, threshold ($F$) or number of photons for rate
computation $m$ can be selected by passing a different value. These parameters
are generally a good starting point for smFRET analysis but can be
tweaked adjusted in
specific cases.
Note that, in the previous burst search, no burst size selection
is was performed
(i.e. the minimum bursts size is
effectively $m$).
An additional parameter $L$ can be passed to apply a threshold on the raw burst
size (before any correction).
We, It is recommended, however,
strongly encourage performing a more accurate burst size selection to select bursts only after the background correction
is applied as shown in the next section~\ref{sec:burstsel}.
In µs-ALEX there are 3 important correction parameters: gamma factor, donor spectral
leakage into the acceptor channel and acceptor direct
excitation~\cite{Lee_2005}. excitation by the donor excitation
laser~\cite{Lee_2005}.
These corrections can be applied by simply
setting assigning to the respective \textit{Data} attributes:
\begin{verbatim}
d.gamma = 0.85
...
\end{verbatim}
These attributes can be assigned either before or after the burst search. In the
latter case,
the existing burst data is automatically updated using the
newly assigned new
correction
values. parameters.
Sometimes it may It might sometimes be useful to specify a fixed threshold, instead
of a threshold
derived from depending on the background
rate like rate, as in the previous example. In
this case, instead of
$F$ we can use $F$, the argument \verb|min_rate_cps|
that
specifies a can be used to
specify the threshold
in Hertz. (in Hertz). For example, a burst search with a 50~kHz
threshold can be performed as follows:
\begin{verbatim}
d.burst_search(min_rate_cps=50e3, m=10, ph_sel=Ph_sel('all'))
\end{verbatim}
Finally, to perform a DCBS burst search (or in general an
AND-gate AND gate burst search,
see section~\ref{sec:burstsearch_intro}) the plugin function
\href{http://fretbursts.readthedocs.org/en/latest/plugins.html#fretbursts.burstlib\_ext.burst\_search\_and\_gate}{\texttt{burst\_search\_and\_gate}}
can be used
like as in the following example:
\begin{verbatim}
d_dcbs = bext.burst_search_and_gate(d, F=6, m=10)
\end{verbatim}
Note
that that, in this
case case, a copy of the \verb|Data| variable
is returned (here called \verb|d_dcbp|)
containing (containing the results
of the new burst
search. search) is returned (called here \verb|d_dcbs|).
In order to
save RAM, reduce memory usage, FRETBursts shares the read-only arrays timestamps and detectors between
different copies of a \verb|Data| object (for example \verb|d| and
\verb|d_dcbs|), while all the \verb|d_dcbs|).
All other data (including background and burst data)
is are copied.
\paragraph{Python details}
The function \verb|burst_search_and_gate|
provides additional arguments accepts optional arguments,
\verb|ph_sel1| and
\verb|ph_sel2| \verb|ph_sel2|, whose
defaults default values correspond to the
classical DCBS photon stream selection (see section~\ref{sec:burstsearch_intro}).
These arguments can be specified to select different photon streams than in
a classical DCBS.
